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(-) Description

Title :  CRYSTAL STRUCTURE OF RIBONUCLEASE SA2 WITH 3'-GMP OBTAINED BY LIGAND DIFFUSION
 
Authors :  V. Bauerova-Hlinkova, J. Sevcik
Date :  14 May 08  (Deposition) - 26 May 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Ribonuclease, Mononucleotide, Protein-Mononucleotide Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Bauerova-Hlinkova, R. Dvorsky, D. Perecko, F. Povazanec, J. Sevci
Structure Of Rnase Sa2 Complexes With Mononucleotides - New Aspects Of Catalytic Reaction And Substrate Recognition
Febs J. V. 276 4156 2009
PubMed-ID: 19558492  |  Reference-DOI: 10.1111/J.1742-4658.2009.07125.X

(-) Compounds

Molecule 1 - RIBONUCLEASE
    Chains: A, B, C
    EC Number: 3.1.4.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEH200
    Expression System Strain: NOVABLUE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: STREPTOMYCES AUREOFACIENS
    Organism Taxid: 1894
    Strain: R8/12
    Synonym: RIBONUCLEASE SA2

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
13GP1Ligand/IonGUANOSINE-3'-MONOPHOSPHATE
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
13GP-1Ligand/IonGUANOSINE-3'-MONOPHOSPHATE
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
13GP1Ligand/IonGUANOSINE-3'-MONOPHOSPHATE
2SO41Ligand/IonSULFATE ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
13GP-1Ligand/IonGUANOSINE-3'-MONOPHOSPHATE
2SO4-1Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:34 , GLU A:56 , ARG A:67 , ARG A:71 , HIS A:86 , TYR A:87 , ARG C:45BINDING SITE FOR RESIDUE SO4 A 98
2AC2SOFTWARESER A:15 , HOH A:139 , GLU B:43 , ARG B:45BINDING SITE FOR RESIDUE SO4 B 98
3AC3SOFTWAREVAL B:37 , VAL B:38 , PHE B:39 , GLU B:40 , ASN B:41 , ARG B:42 , GLU B:43 , GLU B:56 , ARG B:67 , ARG B:71 , HIS B:86 , TYR B:87BINDING SITE FOR RESIDUE 3GP B 99

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:9 -A:97
2B:9 -B:97
3C:9 -C:97

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:28 -Pro A:29
2Gly B:28 -Pro B:29
3Gly C:28 -Pro C:29

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D4A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3D4A)

(-) Exons   (0, 0)

(no "Exon" information available for 3D4A)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:95
 aligned with Q53752_STRAU | Q53752 from UniProtKB/TrEMBL  Length:163

    Alignment length:95
                                    78        88        98       108       118       128       138       148       158     
         Q53752_STRAU    69 PALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTPGSNDRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC 163
               SCOP domains d3d4aa_ A: automated matches                                                                    SCOP domains
               CATH domains 3d4aA00 A:3-97  [code=3.10.450.30, no name defined]                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.hhhhhhhhhhhhhhhhh..........ee..............eeeee............eeee.....eeee.......eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 3d4a A   3 PALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTPGSNDRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC  97
                                    12        22        32        42        52        62        72        82        92     


Chain B from PDB  Type:PROTEIN  Length:95
 aligned with Q53752_STRAU | Q53752 from UniProtKB/TrEMBL  Length:163

    Alignment length:97
                                    76        86        96       106       116       126       136       146       156       
         Q53752_STRAU    67 ADPALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTPGSNDRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC 163
               SCOP domains d3d4ab_ B: automated matches                                                                      SCOP domains
               CATH domains 3d4aB00 B:1-97  [code=3.10.450.30, no name defined]                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.hhhhhhhhhhhhhhhh............................eeee.....--.....eeee.....eeee.......eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 3d4a B   1 ADPALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTPG--DRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC  97
                                    10        20        30        40        50        60  |  |  70        80        90       
                                                                                         63 66                               


Chain C from PDB  Type:PROTEIN  Length:89
 aligned with Q53752_STRAU | Q53752 from UniProtKB/TrEMBL  Length:163

    Alignment length:93
                                    80        90       100       110       120       130       140       150       160   
         Q53752_STRAU    71 LADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTPGSNDRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC 163
               SCOP domains d3d4ac_ C: automated matches                                                                  SCOP domains
               CATH domains 3d4aC00 C:5-97  [code=3.10.450.30, no name defined]                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.hhhhhhhhhhhhhhhhh.........eee..............eeeee....----....eeee.....eeee.......eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 3d4a C   5 LADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTP----RGTRRVVTGGYGEQYWSPDHYATFQEIDPRC  97
                                    14        24        34        44        54       | -  |     74        84        94   
                                                                                    62   67
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D4A)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q53752_STRAU | Q53752)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004521    endoribonuclease activity    Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q53752_STRAU | Q53752: 1py3 1pyl 3d5g 3d5i 3dgy 3dh2

(-) Related Entries Specified in the PDB File

1gmp STRUCTURE OF RIBONUCLEASE SA WITH 2'-GMP
1py3 STRUCTURE OF RIBONUCLEASE SA2 WITHOUT LIGAND
1pyl STRUCTURE OF RIBONUCLEASE SA2 WITHOUT LIGAND
1rsn STRUCTURE OF RIBONUCLEASE SA WITH EXO-2',3'- CYCLOPHOSPHOROTIOATE
2sar STRUCTURE OF RIBONUCLEASE SA WITH 3'-GMP
3d5g
3d5i